Related papers: Twelve years of SAMtools and BCFtools
Software Bills of Material (SBOMs), which improve transparency by listing the components constituting software, are a key countermeasure to the mounting problem of Software Supply Chain attacks. SBOM generation tools take project source…
We develop a cross-platform open-source Java application (BACOM2) with graphic user interface (GUI), and users also can use a XML file to set the parameters of algorithm model, file paths and the dataset of paired samples. BACOM2 implements…
BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
Metadata play a crucial role in adopting the FAIR principles for research software and enables findability and reusability. However, creating high-quality metadata can be resource-intensive for researchers and research software engineers.…
Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data…
The authors' "metatools" are a collection of tools for generic programming. This includes generating Java sources from mathematically well-founded specifications, as well as the creation of strictly typed document object models for XML…
Over the past decade there has been a significant growth in bioinformatics databases, tools and resources. Although, bioinformatics is becoming more specific, increasing the number of bioinformatics-wares has made it difficult for…
Extracting sections from clinical notes is crucial for downstream analysis but is challenging due to variability in formatting and labor-intensive nature of manual sectioning. While proprietary large language models (LLMs) have shown…
Scientific Workflow Systems (SWSs) such as Nextflow have become essential software frameworks for conducting reproducible, scalable, and portable computational analyses in data-intensive fields like genomics, transcriptomics, and…
Augmenting Large Language Models (LLMs) with external tools enables them to execute complex, multi-step tasks. However, tool learning is hampered by the static synthetic data pipelines where data generation and model training are executed…
SModelS is an automatised tool enabling the fast interpretation of simplified model results from the LHC within any model of new physics respecting a $\mathbb{Z}_2$ symmetry. With the version 1.2 we announce several new features. First,…
1. Natural sounds have been recorded for millions of hours over the previous decades using passive acoustic monitoring. Improvements in deep learning models have vastly accelerated the analysis of large portions of this data. While new…
In the era of big and ubiquitous data, professionals and students alike are finding themselves needing to perform a number of textual analysis tasks. Historically, the general lack of statistical expertise and programming skills has stopped…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Many modern cheminformatics workflows derive datasets from ChEMBL, but few of these datasets are published with accompanying code for their generation. Consequently, their methodologies (e.g., selection, filtering, aggregation) are opaque,…
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application…
Large Language Models (LLMs) can enhance their capabilities as AI assistants by integrating external tools, allowing them to access a wider range of information. While recent LLMs are typically fine-tuned with tool usage examples during…